Cited by 262RNA and protein synthesis mechanismsBacterial Genetics and BiotechnologyGenomics and Phylogenetic Studies

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Nonrandom utilization of codon pairs in Escherichia coli.

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Gutman, G A, Hatfield, G W·1989·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.86.10.3699PMC PMC287207

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Abstract

We have analyzed protein-coding sequences of Escherichia coli and find that codon-pair utilization is highly biased, reflecting overrepresentation or underrepresentation of many pairs compared with their random expectations. This effect is over and above that contributed by nonrandomness in the use of amino acid pairs, which itself is highly evident; it is much weaker when nonadjacent codon pairs are examined and virtually disappears when pairs separated by two or three intervening codons are evaluated. There appears to be a high degree of directionality in this bias: any codon that participates in many nonrandom pairs tends to make both over- and underrepresented pairs, but preferentially as a left- or right-hand member. We show a relationship between codon-pair utilization patterns and levels of gene expression: genes encoding proteins expressed at high levels tend to contain more abundant, but more highly underrepresented, codon pairs, relative to genes expressed at low levels. The nonrandom utilization of codon pairs may be a consequence of their effects on translational efficiency, which in turn may be related to the compatibility of adjacent aminoacyl-tRNA isoacceptors at the A and P sites of a translating ribosome.

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Authors: Gutman, G. A., & Hatfield, G. W.
Affiliations: University of California, Irvine (US)
Venue: Proceedings of the National Academy of Sciences
Publisher: National Academy of Sciences
Published: 1989-05
Volume: 86
Issue: 10
Pages: 3699-3703
ISSN: 0027-8424 (ISSN-L)
1091-6490
DOI: 10.1073/pnas.86.10.3699
PMC: PMC287207
OpenAlex: W2063504601
Semantic Scholar: 2e078282edbdc0cc228e53846cc1e546a9101d97
Cited by: 261
References: 38
Citations by year: 2026: 4 · 2025: 1 · 2024: 6 · 2023: 6 · 2022: 9 · 2021: 16 · 2020: 14 · 2019: 16 · 2018: 8 · 2017: 17 · 2016: 11 · 2015: 14 · 2014: 11 · 2013: 7 · 2012: 12
FWCI: 2.73
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Proceedings of the National Academy of Sciences (publishedVersion)
PubMed (publishedVersion)
PubMed Central (submittedVersion)
Funders: University of Southern California
U.S. Public Health Service
University of California, San Diego
National Institute of General Medical Sciences (GM24330)
National Institute of Allergy and Infectious Diseases (AI-21366)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: codon pair bias, Escherichia coli, gene expression levels, translation efficiency, protein-coding sequences, codon usage
MeSH terms: Bacterial Proteins, Codon, DNA, Bacterial, Escherichia coli, Gene Expression Regulation, Genes, Bacterial, Peptide Chain Termination, Translational, Probability, RNA, Messenger

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Nonrandom utilization of codon pairs in Escherichia coli.

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